9O6G | pdb_00009o6g

Wildtype rabbit TRPV5 in nanodics in the presence of Menthol and PI(4,5)P2

PDB DOI: https://doi.org/10.2210/pdb9O6G/pdb
EM Map EMD-70173: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Oryctolagus cuniculus
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2025-04-13 Released: 2026-04-22
Deposition Author(s): De Jesus-Perez, J.J., Moiseenkova-Bell, V.Y.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.37 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9O6G

This is version 1.0 of the entry. See complete history.

Literature

Molecular mechanism of action of menthol, a novel inhibitor of TRPV5 channels

Mendez-Resendiz, A., De Jesus-Perez, J.J., Rangel-Yescas, G.E., Rosenbaum, T., Moiseenkova-Bell, V.Y., Islas, D.L.

To be published.

Macromolecule Content

Total Structure Weight: 353.58 kDa
Atom Count: 20,263
Modeled Residue Count: 2,436
Deposited Residue Count: 2,956
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily V member 5	A, B, C, D	739	Oryctolagus cuniculus	Mutation(s): 0 Gene Names: Trpv5, Ecac1
UniProt
Find proteins for Q9XSM3 (Oryctolagus cuniculus) Explore Q9XSM3 Go to UniProtKB: Q9XSM3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9XSM3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CPL Query on CPL Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain R [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain EA [auth D] SDF format, chain DA [auth D] SDF format, chain CA [auth D] SDF format, chain AA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain R [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain R [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] CA [auth D] DA [auth D] EA [auth D] F [auth A] AA [auth D], CA [auth D], DA [auth D], EA [auth D], F [auth A], G [auth A], H [auth A], J [auth A], N [auth B], O [auth B], P [auth B], R [auth B], U [auth C], V [auth C], W [auth C], Z [auth D]	1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₂ H₈₀ N O₈ P JLPULHDHAOZNQI-ZTIMHPMXSA-N		Interactions Focus chain AA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Z [auth D]
PIO Query on PIO Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain S [auth B] SDF format, chain K [auth A] SDF format, chain GA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain S [auth B] MOL2 format, chain K [auth A] MOL2 format, chain GA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain S [auth B] mmCIF format, chain K [auth A] mmCIF format, chain GA [auth D]	GA [auth D], K [auth A], S [auth B], Y [auth C]	[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate C₂₅ H₄₉ O₁₉ P₃ XLNCEHRXXWQMPK-MJUMVPIBSA-N		Interactions Focus chain GA [auth D] Focus chain K [auth A] Focus chain S [auth B] Focus chain Y [auth C] Interactions & Density Focus chain GA [auth D] Focus chain K [auth A] Focus chain S [auth B] Focus chain Y [auth C]
ERG Query on ERG Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain T [auth C] SDF format, chain Q [auth B] SDF format, chain M [auth B] SDF format, chain I [auth A] SDF format, chain FA [auth D] SDF format, chain E [auth A] SDF format, chain BA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain BA [auth D]	BA [auth D] E [auth A] FA [auth D] I [auth A] M [auth B] BA [auth D], E [auth A], FA [auth D], I [auth A], M [auth B], Q [auth B], T [auth C], X [auth C]	ERGOSTEROL C₂₈ H₄₄ O DNVPQKQSNYMLRS-APGDWVJJSA-N		Interactions Focus chain BA [auth D] Focus chain E [auth A] Focus chain FA [auth D] Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain X [auth C] Interactions & Density Focus chain BA [auth D] Focus chain E [auth A] Focus chain FA [auth D] Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain X [auth C]
IT9 (Subject of Investigation/LOI) Query on IT9 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	(-)-Isopiperitenone C₁₀ H₁₄ O SEZLYIWMVRUIKT-SECBINFHSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.37 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:
RECONSTRUCTION	cryoSPARC	4.4.1

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-22

Deposition Author(s):

De Jesus-Perez, J.J.

Moiseenkova-Bell, V.Y.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM144120

Revision History (Full details and data files)

Version 1.0: 2026-04-22
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.